Merge pull request #91 from neutrons/reduce_two_samples

Reduce two samples

docs/releasenotes/index.rst

@@ -12,6 +12,7 @@ Notes for major and minor releases. Notes for Patch releases are deferred.
 
 **Of interest to the User**:
 
+- PR #91: Add ability to reduce multiple samples from the same run
 - PR #104: Update Mantid version to 6.10
 - PR #95: Optional dead-time correction (disabled by default)
 

reflectivity_ui/interfaces/data_handling/data_set.py

@@ -174,10 +174,32 @@ def set_parameter(self, param, value):
             logging.error("Could not set parameter %s %s", param, value)
         return has_changed
 
-    def calculate_reflectivity(self, direct_beam=None, configuration=None):
+    def calculate_reflectivity(self, direct_beam=None, configuration=None, ws_suffix: str = ""):
         """
         Loop through the cross-section data sets and update
         the reflectivity.
+
+        Parameters
+        ----------
+        direct_beam: CrossSectionData | None
+            Direct beam data
+        configuration: Configuration | None
+            The configuration
+        ws_suffix: str
+            String to add to reflectivity workspace name
+
+        Example
+        -------
+        `ws_suffix` is used when reducing multiple ROIs for the same run and cross-section, to
+        differentiate the workspace names in the Mantid data service
+
+        peak_index = 2
+        # update the active reduction list
+        data_manager.set_active_reduction_list_index(peak_index)
+        # get the first data set of the active reduction list
+        nexus_data = data_manager.reduction_list[0]
+        # calculate the reflectivity for this data set
+        nexus_data.calculate_reflectivity(ws_suffix=str(peak_index))
         """
         if configuration is not None:
             self.configuration = copy.deepcopy(configuration)
@@ -282,6 +304,8 @@ def _as_ints(a):
         )
         _ws = ws if len(ws_list) > 1 else [ws]
         for xs in _ws:
+            # add suffix to avoid overwriting ws in mantid data service, needed for multiple peaks
+            api.RenameWorkspace(str(xs), str(xs) + ws_suffix)
             xs_id = xs.getRun().getProperty("cross_section_id").value
             self.cross_sections[xs_id].q = xs.readX(0)[:].copy()
             self.cross_sections[xs_id]._r = np.ma.masked_equal(xs.readY(0)[:].copy(), 0)

reflectivity_ui/interfaces/data_handling/processing_workflow.py

@@ -36,7 +36,7 @@
     format_5cols=False,
     output_sample_size=10,
     output_directory="",
-    output_file_template="(instrument)_{numbers}_{item}_{state}.{type}",
+    output_file_template="{instrument}_{numbers}_{peak}_{item}_{state}.{type}",
     email_send=False,
     email_zip_data=False,
     email_send_plots=False,
@@ -70,23 +70,34 @@ def execute(self, progress=None):
         if not self.data_manager.reduction_states:
             return
 
-        if self.output_options["export_specular"]:
-            if progress is not None:
-                progress(10, "Computing reflectivity")
-            self.specular_reflectivity()
+        # store current peak shown in the UI
+        active_peak = self.data_manager.active_reduction_list_index
+
+        for peak_index in self.data_manager.peak_reduction_lists.keys():
+            # set active data based on peak index
+            self.data_manager.set_active_reduction_list_index(peak_index)
+            self.data_manager.set_active_data_from_reduction_list(0)
+
+            if self.output_options["export_specular"]:
+                if progress is not None:
+                    progress(10, "Computing reflectivity")
+                self.specular_reflectivity()
+
+            if self.output_options["export_offspec"] or self.output_options["export_offspec_smooth"]:
+                if progress is not None:
+                    progress(20, "Computing off-specular reflectivity")
+                self.offspec(
+                    raw=self.output_options["export_offspec"], binned=self.output_options["export_offspec_smooth"]
+                )
 
-        if self.output_options["export_offspec"] or self.output_options["export_offspec_smooth"]:
             if progress is not None:
-                progress(20, "Computing off-specular reflectivity")
-            self.offspec(
-                raw=self.output_options["export_offspec"], binned=self.output_options["export_offspec_smooth"]
-            )
+                progress(60, "Computing GISANS")
+            if self.output_options["export_gisans"]:
+                # FIXME 66 - could be an AttributeError from self.gisans().  Catch it!
+                self.gisans(progress=progress)
 
-        if progress is not None:
-            progress(60, "Computing GISANS")
-        if self.output_options["export_gisans"]:
-            # FIXME 66 - could be an AttributeError from self.gisans().  Catch it!
-            self.gisans(progress=progress)
+        # restore current peak shown in the UI
+        self.data_manager.set_active_reduction_list_index(active_peak)
 
         if self.output_options["email_send"]:
             self.send_email()
@@ -112,6 +123,7 @@ def get_file_name(self, run_list=None, pol_state=None, data_type="dat", process_
         if pol_state is not None:
             base_name = base_name.replace("{state}", pol_state)
         base_name = base_name.replace("{type}", data_type)
+        base_name = base_name.replace("{peak}", f"peak{self.data_manager.active_reduction_list_index}")
         return os.path.join(self.output_options["output_directory"], base_name)
 
     def write_quicknxs(self, output_data, output_file_base, xs=None):
@@ -152,7 +164,11 @@ def write_quicknxs(self, output_data, output_file_base, xs=None):
 
             state_output_path = output_file_base.replace("{state}", pol_state)
             quicknxs_io.write_reflectivity_header(
-                self.data_manager.reduction_list, self.data_manager.direct_beam_list, state_output_path, _pol_state
+                self.data_manager.peak_reduction_lists,
+                self.data_manager.active_reduction_list_index,
+                self.data_manager.direct_beam_list,
+                state_output_path,
+                _pol_state,
             )
             quicknxs_io.write_reflectivity_data(
                 state_output_path, output_data[pol_state], col_names, as_5col=five_cols